Tool assembly: NeLS
What is the NeLS data management tool assembly?
The Norwegian e-Infrastructure for Life Sciences (NeLS) is an infrastructure provided by ELIXIR Norway. NeLS provides necessary tools for Data Management and covers Planning, Processing, Analysing and Sharing Data Life Cycle stages and offers Data Storage capacities.
Who can use the NeLS data management tool assembly?
NeLS and the underlying infrastructure are accessible for researchers in Norway and their collaborators. Eligible researchers can apply for storage quotas and get support through the National (Norwegian) bioinformatics support desk email@example.com. Most of the tools in NeLS are open source and can be reused.
For what can you use the NeLS data management tool assembly?
You can access all tools in NeLS using the the national solution for secure login and data sharing in the educational and research sector FEIDE, when coupled with ELIXIR AAI. The NeLS Data Management tool assembly provides support with Data Management Planning through an instance of the Data Steward Wizard following the guidelines of the major national and European funding bodys. Dedicated references guide you through national infrastructure, resources, laws and regulations and also include the Tryggve ELSI Checklist for Ethical, Legal and Social Implications. Soon you will be able to submit storage request forms for Data Storage in NeLS with defined access permissions through the Data Stewardship Wizard.
Data Storage is the core functionality of NeLS and builds upon a 3 layer tiered system: the first layer is intended for short-term storage when computing, processing and analysing data; the second layer of medium capacity (NeLS) is intended for sharing and storing active research data, while the third layer (StoreBioinfo) of high capacity is intended for longer storage until end of a project. Data in the second (NeLS) layer is protected against hardware failure on disk or server level and snapshots of the data are kept for 4 weeks. The third layer is implemented on top of the national research data storage solutions operated by Sigma2 Uninett A/S and is protected against data loss by snapshots and geo-replication. National Norwegian research infrastructures, such as the Norwegian sequencing infrastructure NorSeq can directly upload data to your NeLS project for you.
For Processing and Analysing your data, the NeLS Data Management tool assembly provides access to a national instance of Galaxy with ~2000 tools. Data stored in NeLS is directly available within this Galaxy instance, hence you do not need to keep local copies of your data.
In order to help you keeping track of metadata, NeLS is integrated with the SEEK web-based cataloguing and sharing platform. You can use any instance of SEEK such as the public FAIRDOMHub to manage metadata associated with your data stored in NeLS and access the data through SEEK. SEEK uses the ISA (Investigation, Study, Assay) structure to organise your data and recommended minimal information such as sample characteristics, technologies, measurements and relationships between samples, data and models. Public SEEK instances like the FAIRDOMHub can also be used to collaborate on data and to share them publicly. If you are doing modelling, you can also use the inbuilt JWS Online simulator for your SBML models.
One recommended way to share your data is to deposit them in the ELIXIR Deposition Databases for Biomolecular Data. The NeLS Data Management tool assembly will soon offer tools to help you with the deposition step for data stored in NeLS.
How to write a Data Management Plan (DMP). Data organisation
Best practices to name and organise research data. Data storage
How to find appropriate storage solutions. Data publication
How to prepare data and find repositories for publication. Documentation and metadata
How to document and describe your data.
Relevant tools and resourcesSkip tool table
|Tool or resource||Description||Related pages||Registry|
|Data Stewardship Wizard||Publicly available online tool for composing smart data management plans||Data management plan Researcher Data Steward: research Data Steward: infrastructure TSD Plant Phenomics Plant Genomics||Tool info Training|
|ELIXIR Deposition Databases for Biomolecular Data||List of discipline-specific deposition databases recommended by ELIXIR.||Data publication Researcher Data Steward: research Data Steward: infrastructure COVID-19 Data Portal IFB CSC||Standards/Databases|
|ELIXIR-AAI||The ELIXIR Authentication and Authorisation Infrastructure (AAI)||Sensitive data TSD TransMed||Training|
|FAIRDOM-SEEK||A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes.||Data storage Data Steward: infrastructure Microbial biotechnology IFB Machine actionability Plant Phenomics Plant Genomics||Tool info Training|
|FAIRDOMHub||Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models, etc. (public SEEK instance)||Data storage Researcher Documentation and metadata Microbial biotechnology Machine actionability Data Steward: research||Standards/Databases|
|Galaxy||Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.||Marine Metagenomics Data analysis Researcher Data Steward: infrastructure IFB Galaxy||Tool info Training|
|Tryggve ELSI Checklist||A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects||Sensitive data Data Steward: policy Data Steward: research Human data CSC TSD Data protection|
Feide is the national solution for secure login and data exchange in education and research. Feide can be linked with ELIXIR-AAI through eduGAIN.
|TSD Marine Metagenomics|
DS-Wizard is a tool to aid the creation, organisaton and sharing of data management plans. It provides scientists with guidance, facilitating the understanding of the key components of FAIR-oriented Data Stewardship. The template in this instance provides additional guidance on resources, laws and regulations in Norway.
Data Stewardship Wizard
|TSD Marine Metagenomics Data management plan|
Galaxy is an open source, web-based platform for data intensive biomedical research. This instance of Galaxy is coupled with NeLS for easy data transfer.
|Data analysis Sensitive data Existing data Data publication|
Norwegian e-Infrastructure for Life Sciences enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their omics-scale data.
The National Infrastructure for Research Data (NIRD) infrastructure offers storage services, archiving services, and processing capacity for computing on the stored data. It offers services and capacities to any scientific discipline that requires access to advanced, large-scale, or high-end resources for storing, processing, publishing research data or searching digital databases and collections. This service is owned and operatedby Sigma2 NRIS, which is a joint collaboration between UiO, UiB, NTNU, UiT, and UNINETT Sigma2.
|Data transfer Data storage|